{
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  "Package": "rGREAT",
  "Type": "Package",
  "Title": "GREAT Analysis - Functional Enrichment on Genomic Regions",
  "Version": "2.15.0",
  "Date": "2026-01-30",
  "Authors@R": "person(\"Zuguang\", \"Gu\", email = \"guzuguang@suat-sz.edu.cn\", role = c(\"aut\", \"cre\"),\ncomment = c('ORCID'=\"0000-0002-7395-8709\"))",
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  "biocViews": "GeneSetEnrichment, GO, Pathways, Software, Sequencing,\nWholeGenome, GenomeAnnotation, Coverage",
  "Description": "GREAT (Genomic Regions Enrichment of Annotations Tool) is\na type of functional enrichment analysis directly performed on\ngenomic regions. This package implements the GREAT algorithm\n(the local GREAT analysis), also it supports directly\ninteracting with the GREAT web service (the online GREAT\nanalysis). Both analysis can be viewed by a Shiny application.\nrGREAT by default supports more than 600 organisms and a large\nnumber of gene set collections, as well as self-provided gene\nsets and organisms from users. Additionally, it implements a\ngeneral method for dealing with background regions.",
  "URL": "https://github.com/jokergoo/rGREAT,\nhttp://great.stanford.edu/public/html/",
  "License": "MIT + file LICENSE",
  "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:40:34 UTC",
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  "Packaged": {
    "Date": "2026-11-01 13:21:56 UTC",
    "User": "root"
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  "Author": "Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>)",
  "Maintainer": "Zuguang Gu <guzuguang@suat-sz.edu.cn>",
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  "_created": "2026-11-01T13:21:56.000Z",
  "_published": "2026-11-01T15:11:27.906Z",
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  "_homeurl": "https://github.com/jokergoo/rgreat",
  "_realowner": "bioc",
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  "_exports": [
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    "availableOntologies",
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    "extendTSSFromDataFrame",
    "extendTSSFromOrgDb",
    "extendTSSFromTxDb",
    "getEnrichmentTable",
    "getEnrichmentTables",
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    "getGeneSetsFromOrgDb",
    "getGenesFromGencode",
    "getGenomeDataFromNCBI",
    "getGREATDefaultTSS",
    "getKEGGGenome",
    "getKEGGPathways",
    "getRefSeqGenesFromUCSC",
    "getRegionGeneAssociations",
    "getTSS",
    "great",
    "great_opt",
    "GreatJob",
    "GreatObject",
    "plotRegionGeneAssociationGraphs",
    "plotRegionGeneAssociations",
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    "read_gmt",
    "shinyReport",
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  "_help": [
    {
      "page": "availableCategories-GreatJob-method",
      "title": "Available ontology categories of the GREAT job",
      "topics": [
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        "availableCategories,GreatJob-method"
      ]
    },
    {
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      "title": "All available ontology names of the GREAT job",
      "topics": [
        "availableOntologies",
        "availableOntologies,GreatJob-method"
      ]
    },
    {
      "page": "extendTSS",
      "title": "Extend TSS",
      "topics": [
        "extendTSS"
      ]
    },
    {
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      "title": "Extend TSS",
      "topics": [
        "extendTSSFromDataFrame"
      ]
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    {
      "page": "extendTSSFromOrgDb",
      "title": "Extend TSS",
      "topics": [
        "extendTSSFromOrgDb"
      ]
    },
    {
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      "title": "Extend TSS",
      "topics": [
        "extendTSSFromTxDb"
      ]
    },
    {
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      "title": "Method dispatch page for getEnrichmentTable",
      "topics": [
        "getEnrichmentTable"
      ]
    },
    {
      "page": "getEnrichmentTable-GreatJob-method",
      "title": "Get a single enrichment table from GREAT web server",
      "topics": [
        "getEnrichmentTable,GreatJob-method"
      ]
    },
    {
      "page": "getEnrichmentTable-GreatObject-method",
      "title": "Get enrichment table",
      "topics": [
        "getEnrichmentTable,GreatObject-method"
      ]
    },
    {
      "page": "getEnrichmentTables-dispatch",
      "title": "Method dispatch page for getEnrichmentTables",
      "topics": [
        "getEnrichmentTables"
      ]
    },
    {
      "page": "getEnrichmentTables-GreatJob-method",
      "title": "Get enrichment tables from GREAT web server",
      "topics": [
        "getEnrichmentTables,GreatJob-method"
      ]
    },
    {
      "page": "getEnrichmentTables-GreatObject-method",
      "title": "Get enrichment table",
      "topics": [
        "getEnrichmentTables,GreatObject-method"
      ]
    },
    {
      "page": "getGapFromUCSC",
      "title": "Get gap regions from UCSC",
      "topics": [
        "getGapFromUCSC"
      ]
    },
    {
      "page": "getGeneSetsFromBioMart",
      "title": "Get GO gene sets from BioMart",
      "topics": [
        "getGeneSetsFromBioMart"
      ]
    },
    {
      "page": "getGeneSetsFromOrgDb",
      "title": "Get GO gene sets from OrgDb object",
      "topics": [
        "getGeneSetsFromOrgDb"
      ]
    },
    {
      "page": "getGenesFromGencode",
      "title": "Get Gencode genes",
      "topics": [
        "getGenesFromGencode"
      ]
    },
    {
      "page": "getGenomeDataFromNCBI",
      "title": "Get genome data from NCBI",
      "topics": [
        "getGenomeDataFromNCBI"
      ]
    },
    {
      "page": "getGREATDefaultTSS",
      "title": "Get built-in TSS from GREAT",
      "topics": [
        "getGREATDefaultTSS"
      ]
    },
    {
      "page": "getKEGGGenome",
      "title": "Get the corresponding assembly id for a kegg organism",
      "topics": [
        "getKEGGGenome"
      ]
    },
    {
      "page": "getKEGGPathways",
      "title": "Get KEGG pathway gene sets",
      "topics": [
        "getKEGGPathways"
      ]
    },
    {
      "page": "getRefSeqGenesFromUCSC",
      "title": "Get RefSeq genes from UCSC",
      "topics": [
        "getRefSeqGenesFromUCSC"
      ]
    },
    {
      "page": "getRegionGeneAssociations-dispatch",
      "title": "Method dispatch page for getRegionGeneAssociations",
      "topics": [
        "getRegionGeneAssociations"
      ]
    },
    {
      "page": "getRegionGeneAssociations-GreatJob-method",
      "title": "Get region-gene associations",
      "topics": [
        "getRegionGeneAssociations,GreatJob-method"
      ]
    },
    {
      "page": "getRegionGeneAssociations-GreatObject-method",
      "title": "Get region-gene associations",
      "topics": [
        "getRegionGeneAssociations,GreatObject-method"
      ]
    },
    {
      "page": "getTSS",
      "title": "Get the internally used TSS",
      "topics": [
        "getTSS"
      ]
    },
    {
      "page": "great",
      "title": "Perform GREAT analysis",
      "topics": [
        "great"
      ]
    },
    {
      "page": "great_opt",
      "title": "Global parameters for rGREAT",
      "topics": [
        "great_opt"
      ]
    },
    {
      "page": "GreatJob",
      "title": "Constructor method for GreatJob class",
      "topics": [
        "GreatJob"
      ]
    },
    {
      "page": "GreatJob-class",
      "title": "Class to store and retrieve GREAT results",
      "topics": [
        "GreatJob-class"
      ]
    },
    {
      "page": "GreatObject",
      "title": "Constructor method for GreatObject class",
      "topics": [
        "GreatObject"
      ]
    },
    {
      "page": "GreatObject-class",
      "title": "Class for local GREAT analysis",
      "topics": [
        "GreatObject-class"
      ]
    },
    {
      "page": "plotRegionGeneAssociationGraphs-GreatJob-method",
      "title": "Plot region-gene associations",
      "topics": [
        "plotRegionGeneAssociationGraphs",
        "plotRegionGeneAssociationGraphs,GreatJob-method"
      ]
    },
    {
      "page": "plotRegionGeneAssociations-dispatch",
      "title": "Method dispatch page for plotRegionGeneAssociations",
      "topics": [
        "plotRegionGeneAssociations"
      ]
    },
    {
      "page": "plotRegionGeneAssociations-GreatJob-method",
      "title": "Plot region-gene associations",
      "topics": [
        "plotRegionGeneAssociations,GreatJob-method"
      ]
    },
    {
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